The X-ray structure of photosystem II reveals a novel electron transport pathway between P680, cytochrome b₅₅₉ and the energy-quenching cation, Chl_Z⁺

When water oxidation by photosystem II (PSII) is impaired, an oxidized chlorophyll (Chl_Z⁺) is formed that quenches excitation and may prevent photodamage. Both the identification of this Chl⁺ and the mechanism of its oxidation and reduction are controversial. Using the available X-ray structures of PSII we calculated the efficiency of two proposed quenchers, Chl_Z⁺(D1) and Chl_Z⁺(D2). Of these two, only Chl_Z⁺(D1) can quench to the degree observed experimentally. We also identify a chain of closely spaced pigments in the structure from Thermosynechococcus vulcanus that we propose to form a novel electron transport pathway between Chl_Z(D1), β-carotene, P680⁺ and cytochrome b₅₅₉.